SuperPred: drug classification and target prediction

The drug classification scheme of the World Health Organization (WHO) [Anatomical Therapeutic Chemical (ATC)-code] connects chemical classification and therapeutic approach. It is generally accepted that compounds with similar physicochemical properties exhibit similar biological activity. If this hypothesis holds true for drugs, then the ATC-code, the putative medical indication area and potentially the medical target should be predictable on the basis of structural similarity. We have validated that the prediction of the drug class is reliable for WHO-classified drugs. The reliability of the predicted medical effects of the compounds increases with a rising number of (physico-) chemical properties similar to a drug with known function. The web-server translates a user-defined molecule into a structural fingerprint that is compared to about 6300 drugs, which are enriched by 7300 links to molecular targets of the drugs, derived through text mining followed by manual curation. Links to the affected pathways are provided. The similarity to the medical compounds is expressed by the Tanimoto coefficient that gives the structural similarity of two compounds. A similarity score higher than 0.85 results in correct ATC prediction for 81% of all cases. As the biological effect is well predictable, if the structural similarity is sufficient, the web-server allows prognoses about the medical indication area of novel compounds and to find new leads for known targets

Euclid preparation: XXVII. A UV-NIR spectral atlas of compact planetary nebulae for wavelength calibration

The Euclid mission will conduct an extragalactic survey over 15 000 deg2 of the extragalactic sky. The spectroscopic channel of the Near-Infrared Spectrometer and Photometer (NISP) has a resolution of R~450 for its blue and red grisms that collectively cover the 0.93-1.89 μm range. NISP will obtain spectroscopic redshifts for 3 107 galaxies for the experiments on galaxy clustering, baryonic acoustic oscillations, and redshift space distortion. The wavelength calibration must be accurate within 5 A to avoid systematics in the redshifts and downstream cosmological parameters. The NISP pre-flight dispersion laws for the grisms were obtained on the ground using a Fabry-Perot etalon. Launch vibrations, zero gravity conditions, and thermal stabilisation may alter these dispersion laws, requiring an in-flight recalibration. To this end, we use the emission lines in the spectra of compact planetary nebulae (PNe), which were selected from a PN database. To ensure completeness of the PN sample, we developed a novel technique to identify compact and strong line emitters in Gaia spectroscopic data using the Gaia spectra shape coefficients. We obtained VLT/X-shooter spectra from 0.3 to 2.5 μm for 19 PNe in excellent seeing conditions and a wide slit, mimicking Euclid's slitless spectroscopy mode but with a ten times higher spectral resolution. Additional observations of one northern PN were obtained in the 0.80- 1.90 μm range with the GMOS and GNIRS instruments at the Gemini North Observatory. The collected spectra were combined into an atlas of heliocentric vacuum wavelengths with a joint statistical and systematic accuracy of 0.1 A in the optical and 0.3 A in the near-infrared. The wavelength atlas and the related 1D and 2D spectra are made publicly available

Euclid preparation: XXX. Performance assessment of the NISP red grism through spectroscopic simulations for the wide and deep surveys

This work focusses on the pilot run of a simulation campaign aimed at investigating the spectroscopic capabilities of the Euclid Near-Infrared Spectrometer and Photometer (NISP), in terms of continuum and emission line detection in the context of galaxy evolutionary studies. To this purpose, we constructed, emulated, and analysed the spectra of 4992 star-forming galaxies at 0:3 ≥ z ≥ 2:5 using the NISP pixel-level simulator. We built the spectral library starting from public multi-wavelength galaxy catalogues, with value-added information on spectral energy distribution (SED) fitting results, and stellar population templates from Bruzual & Charlot (2003, MNRAS, 344, 1000). Rest-frame optical and near-IR nebular emission lines were included using empirical and theoretical relations. Dust attenuation was treated using the Calzetti extinction law accounting for the differential attenuation in line-emitting regions with respect to the stellar continuum. The NISP simulator was configured including instrumental and astrophysical sources of noise such as the dark current, read-out noise, zodiacal background, and out-of-field stray light. In this preliminary study, we avoided contamination due to the overlap of the slitless spectra. For this purpose, we located the galaxies on a grid and simulated only the first order spectra.We inferred the 3.5δ NISP red grism spectroscopic detection limit of the continuum measured in the H band for star-forming galaxies with a median disk half-light radius of 0: 004 at magnitude H = 19:5 = 0:2ABmag for the Euclid Wide Survey and at H = 20:8 = 0:6ABmag for the Euclid Deep Survey. We found a very good agreement with the red grism emission line detection limit requirement for the Wide and Deep surveys. We characterised the effect of the galaxy shape on the detection capability of the red grism and highlighted the degradation of the quality of the extracted spectra as the disk size increased. In particular, we found that the extracted emission line signal-to-noise ratio (S/N) drops by 45% when the disk size ranges from 0: 0025 to 100. These trends lead to a correlation between the emission line S/N and the stellar mass of the galaxy and we demonstrate the effect in a stacking analysis unveiling emission lines otherwise too faint to detect

Euclid preparation: VIII. The Complete Calibration of the Colour–Redshift Relation survey: VLT/KMOS observations and data release

The Complete Calibration of the Colour–Redshift Relation survey (C3R2) is a spectroscopic effort involving ESO and Keck facilities designed specifically to empirically calibrate the galaxy colour–redshift relation – P(z|C) to the Euclid depth (iAB = 24.5) and is intimately linked to the success of upcoming Stage IV dark energy missions based on weak lensing cosmology. The aim is to build a spectroscopic calibration sample that is as representative as possible of the galaxies of the Euclid weak lensing sample. In order to minimise the number of spectroscopic observations necessary to fill the gaps in current knowledge of the P(z|C), self-organising map (SOM) representations of the galaxy colour space have been constructed. Here we present the first results of an ESO@VLT Large Programme approved in the context of C3R2, which makes use of the two VLT optical and near-infrared multi-object spectrographs, FORS2 and KMOS. This data release paper focuses on high-quality spectroscopic redshifts of high-redshift galaxies observed with the KMOS spectrograph in the near-infrared H- and K-bands. A total of 424 highly-reliable redshifts are measured in the 1.3 ≤ z ≤ 2.5 range, with total success rates of 60.7% in the H-band and 32.8% in the K-band. The newly determined redshifts fill 55% of high (mainly regions with no spectroscopic measurements) and 35% of lower (regions with low-resolution/low-quality spectroscopic measurements) priority empty SOM grid cells. We measured Hα fluxes in a 1.″2 radius aperture from the spectra of the spectroscopically confirmed galaxies and converted them into star formation rates. In addition, we performed an SED fitting analysis on the same sample in order to derive stellar masses, E(B − V), total magnitudes, and SFRs. We combine the results obtained from the spectra with those derived via SED fitting, and we show that the spectroscopic failures come from either weakly star-forming galaxies (at z   2 galaxies

Euclid preparation: VII. Forecast validation for Euclid cosmological probes

Aims: The Euclid space telescope will measure the shapes and redshifts of galaxies to reconstruct the expansion history of the Universe and the growth of cosmic structures. The estimation of the expected performance of the experiment, in terms of predicted constraints on cosmological parameters, has so far relied on various individual methodologies and numerical implementations, which were developed for different observational probes and for the combination thereof. In this paper we present validated forecasts, which combine both theoretical and observational ingredients for different cosmological probes. This work is presented to provide the community with reliable numerical codes and methods for Euclid cosmological forecasts. / Methods: We describe in detail the methods adopted for Fisher matrix forecasts, which were applied to galaxy clustering, weak lensing, and the combination thereof. We estimated the required accuracy for Euclid forecasts and outline a methodology for their development. We then compare and improve different numerical implementations, reaching uncertainties on the errors of cosmological parameters that are less than the required precision in all cases. Furthermore, we provide details on the validated implementations, some of which are made publicly available, in different programming languages, together with a reference training-set of input and output matrices for a set of specific models. These can be used by the reader to validate their own implementations if required. / Results: We present new cosmological forecasts for Euclid. We find that results depend on the specific cosmological model and remaining freedom in each setting, for example flat or non-flat spatial cosmologies, or different cuts at non-linear scales. The numerical implementations are now reliable for these settings. We present the results for an optimistic and a pessimistic choice for these types of settings. We demonstrate that the impact of cross-correlations is particularly relevant for models beyond a cosmological constant and may allow us to increase the dark energy figure of merit by at least a factor of three

Euclid preparation: XII. Optimizing the photometric sample of the Euclid survey for galaxy clustering and galaxy-galaxy lensing analyses

Photometric redshifts (photo-zs) are one of the main ingredients in the analysis of cosmological probes. Their accuracy particularly affects the results of the analyses of galaxy clustering with photometrically selected galaxies (GCph) and weak lensing. In the next decade, space missions such as Euclid will collect precise and accurate photometric measurements for millions of galaxies. These data should be complemented with upcoming ground-based observations to derive precise and accurate photo-zs. In this article we explore how the tomographic redshift binning and depth of ground-based observations will affect the cosmological constraints expected from the Euclid mission. We focus on GCph and extend the study to include galaxy-galaxy lensing (GGL). We add a layer of complexity to the analysis by simulating several realistic photo-z distributions based on the Euclid Consortium Flagship simulation and using a machine learning photo-z algorithm. We then use the Fisher matrix formalism together with these galaxy samples to study the cosmological constraining power as a function of redshift binning, survey depth, and photo-z accuracy. We find that bins with an equal width in redshift provide a higher figure of merit (FoM) than equipopulated bins and that increasing the number of redshift bins from ten to 13 improves the FoM by 35% and 15% for GCph and its combination with GGL, respectively. For GCph, an increase in the survey depth provides a higher FoM. However, when we include faint galaxies beyond the limit of the spectroscopic training data, the resulting FoM decreases because of the spurious photo-zs. When combining GCph and GGL, the number density of the sample, which is set by the survey depth, is the main factor driving the variations in the FoM. Adding galaxies at faint magnitudes and high redshift increases the FoM, even when they are beyond the spectroscopic limit, since the number density increase compensates for the photo-z degradation in this case. We conclude that there is more information that can be extracted beyond the nominal ten tomographic redshift bins of Euclid and that we should be cautious when adding faint galaxies into our sample since they can degrade the cosmological constraints

Euclid preparation - VII. Forecast validation for Euclid cosmological probes

Aims. The Euclid space telescope will measure the shapes and redshifts of galaxies to reconstruct the expansion history of the Universe and the growth of cosmic structures. The estimation of the expected performance of the experiment, in terms of predicted constraints on cosmological parameters, has so far relied on various individual methodologies and numerical implementations, which were developed for different observational probes and for the combination thereof. In this paper we present validated forecasts, which combine both theoretical and observational ingredients for different cosmological probes. This work is presented to provide the community with reliable numerical codes and methods for Euclid cosmological forecasts. Methods. We describe in detail the methods adopted for Fisher matrix forecasts, which were applied to galaxy clustering, weak lensing, and the combination thereof. We estimated the required accuracy for Euclid forecasts and outline a methodology for their development. We then compare and improve different numerical implementations, reaching uncertainties on the errors of cosmological parameters that are less than the required precision in all cases. Furthermore, we provide details on the validated implementations, some of which are made publicly available, in different programming languages, together with a reference training-set of input and output matrices for a set of specific models. These can be used by the reader to validate their own implementations if required. Results. We present new cosmological forecasts for Euclid. We find that results depend on the specific cosmological model and remaining freedom in each setting, for example flat or non-flat spatial cosmologies, or different cuts at non-linear scales. The numerical implementations are now reliable for these settings. We present the results for an optimistic and a pessimistic choice for these types of settings. We demonstrate that the impact of cross-correlations is particularly relevant for models beyond a cosmological constant and may allow us to increase the dark energy figure of merit by at least a factor of three

Euclid preparation: XII. Optimizing the photometric sample of the Euclid survey for galaxy clustering and galaxy-galaxy lensing analyses

Photometric redshifts (photo-zs) are one of the main ingredients in the analysis of cosmological probes. Their accuracy particularly affects the results of the analyses of galaxy clustering with photometrically selected galaxies (GCph) and weak lensing. In the next decade, space missions such as Euclid will collect precise and accurate photometric measurements for millions of galaxies. These data should be complemented with upcoming ground-based observations to derive precise and accurate photo-zs. In this article we explore how the tomographic redshift binning and depth of ground-based observations will affect the cosmological constraints expected from the Euclid mission. We focus on GCph and extend the study to include galaxy-galaxy lensing (GGL). We add a layer of complexity to the analysis by simulating several realistic photo-z distributions based on the Euclid Consortium Flagship simulation and using a machine learning photo-z algorithm. We then use the Fisher matrix formalism together with these galaxy samples to study the cosmological constraining power as a function of redshift binning, survey depth, and photo-z accuracy. We find that bins with an equal width in redshift provide a higher figure of merit (FoM) than equipopulated bins and that increasing the number of redshift bins from ten to 13 improves the FoM by 35% and 15% for GCph and its combination with GGL, respectively. For GCph, an increase in the survey depth provides a higher FoM. However, when we include faint galaxies beyond the limit of the spectroscopic training data, the resulting FoM decreases because of the spurious photo-zs. When combining GCph and GGL, the number density of the sample, which is set by the survey depth, is the main factor driving the variations in the FoM. Adding galaxies at faint magnitudes and high redshift increases the FoM, even when they are beyond the spectroscopic limit, since the number density increase compensates for the photo-z degradation in this case. We conclude that there is more information that can be extracted beyond the nominal ten tomographic redshift bins of Euclid and that we should be cautious when adding faint galaxies into our sample since they can degrade the cosmological constraints

Euclid preparation: VIII. The Complete Calibration of the Colour–Redshift Relation survey: VLT/KMOS observations and data release

The Complete Calibration of the Colour–Redshift Relation survey (C3R2) is a spectroscopic effort involving ESO and Keck facilities designed specifically to empirically calibrate the galaxy colour–redshift relation – P(z|C) to the Euclid depth (iAB = 24.5) and is intimately linked to the success of upcoming Stage IV dark energy missions based on weak lensing cosmology. The aim is to build a spectroscopic calibration sample that is as representative as possible of the galaxies of the Euclid weak lensing sample. In order to minimise the number of spectroscopic observations necessary to fill the gaps in current knowledge of the P(z|C), self-organising map (SOM) representations of the galaxy colour space have been constructed. Here we present the first results of an ESO@VLT Large Programme approved in the context of C3R2, which makes use of the two VLT optical and near-infrared multi-object spectrographs, FORS2 and KMOS. This data release paper focuses on high-quality spectroscopic redshifts of high-redshift galaxies observed with the KMOS spectrograph in the near-infrared H- and K-bands. A total of 424 highly-reliable redshifts are measured in the 1.3 ≤ z ≤ 2.5 range, with total success rates of 60.7% in the H-band and 32.8% in the K-band. The newly determined redshifts fill 55% of high (mainly regions with no spectroscopic measurements) and 35% of lower (regions with low-resolution/low-quality spectroscopic measurements) priority empty SOM grid cells. We measured Hα fluxes in a 1. 002 radius aperture from the spectra of the spectroscopically confirmed galaxies and converted them into star formation rates. In addition, we performed an SED fitting analysis on the same sample in order to derive stellar masses, E(B − V), total magnitudes, and SFRs. We combine the results obtained from the spectra with those derived via SED fitting, and we show that the spectroscopic failures come from either weakly star-forming galaxies (at z 2 galaxies